Compositions and methods for detecting mecc-containing methicillin-resistant staphylococcus aureus

ABSTRACT

Methods for the rapid detection of the presence or absence of mecC-containing  Staphylococcus aureus  (mecC-MRSA) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the genes for mecC-MRSA, along with kits are provided that are designed for the detection of mecC-MRSA.

FIELD OF THE INVENTION

The present disclosure relates to the field of bacterial diagnostics,and more particularly to detection of methicillin-resistantStaphylococcus aureus (MRSA) that contain mecC nucleic acid sequences.

BACKGROUND OF THE INVENTION

Staphylococcus aureus (“S. aureus” or “SA”) is a facultative anaerobic,Gram-positive bacterium, whose natural reservoir includes the human skinand nose and can also inhabit wounds. Most people who carry S. aureusshow no sign of infection; however, S. aureus can become invasive andcause infection in the body if the normal barrier is breached. S. aureuscan cause a number of illnesses ranging from minor skin infections suchas pimples, boils, and abscesses, to major diseases such as pneumonia,meningitis, and sepsis. Tissues other than skin and nose can be infectedwhen barriers are breached, e.g., skin or mucosal lining, which leads tofuruncles and carbuncles. S. aureus infections can spread between peoplethrough skin contact with an infected person or contact with objectsused by an infected person.

S. aureus possess a remarkable ability to develop resistance to themajor antibiotics, including the penicillins (methicillin, oxacillin,cloxacillin and flucloxacillin), which has earned it the label“superbug”. Methicillin-resistant S. aureus (MRSA) is a bacterium thathas become resistant to penicillins, and it is responsible for severalhuman infections that are difficult to treat. MRSA may also be known asoxacillin-resistant S. aureus (ORSA) and multiple-resistant S. aureus,while the non-methicillin resistant strains of S. aureus are sometimescalled methicillin-sensitive S. aureus (MSSA).

The gene required for methicillin resistance in staphylococci, mecA,encodes the low-affinity penicillin-binding protein 2a (PBP2a) (Niemeyeret al., J. Bacteriol., (1996), 178(18):5464-5471). A novel variant ofmecA (mecA_(LGA251)), which has been renamed as mecC, was recentlyidentified in S. aureus isolates from both humans and animals (Harrisonet al., Antimicrob. Agents Chemother., (2013), 57(3):1524-1528). Thishomologue shares 70% nucleotide identity with the mecA gene, and itspresence poses diagnostic problems with the potential to be misdiagnosedas methicillin-sensitive S. aureus (Paterson et al., Trends Microbiol.,(2014), 22(1):42-47). Thus there is a need in the art for a quick andreliable method to specifically detect mecC-containing MRSA in asensitive manner.

SUMMARY OF THE INVENTION

Certain embodiments in the present disclosure relate to methods for therapid detection of the presence or absence of mecC-containingStaphylococcus aureus (mecC-MRSA) in a biological or non-biologicalsample, for example, multiplex detection of mecC-MRSA by real-timepolymerase chain reaction in a single test tube. Embodiments includemethods of detection of mecC-MRSA comprising performing at least onecycling step, which may include an amplifying step and a hybridizingstep. Furthermore, embodiments include primers, probes, and kits thatare designed for the detection of mecC-MRSA in a single tube. Thedetection methods are designed to target the mecC gene which allows oneto detect mecC-MRSA in a single test.

In one embodiment, a method for detecting mecC-containing Staphylococcusaureus in a sample is provided, including performing an amplifying stepincluding contacting the sample with an orfX primer and a mecC-MRSAprimer to produce an amplification product if mecC-MRSA is present inthe sample; performing a hybridizing step including contacting theamplification product with one or more detectable mecC-MRSA probes; anddetecting the presence or absence of the amplified product, wherein thepresence of the amplified product is indicative of the presence ofmecC-MRSA in the sample and wherein the absence of the amplified productis indicative of the absence of mecC-MRSA in the sample; wherein theorfX primer comprises or consists of the sequence of SEQ ID NO 9, or acomplement thereof, and the mecC-MRSA primer comprises a sequenceselected from the group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7,and 8, or a complement thereof; and wherein the detectable mecC-MRSAprobe comprises or consists of the sequence of SEQ ID NO: 10, or acomplement thereof.

In one embodiment, the primer set for amplification of the mecC-MRSAgene target include nucleic acid sequences of SEQ ID NOs: 1, 2, 3, 4, 5,6, 7, 8, and 9 or a complement thereof, and the detectable probe fordetection of the mecC-MRSA amplification product includes the nucleicacid sequence of SEQ ID NO: 10.

Other embodiments provide an oligonucleotide comprising or consisting ofa sequence of nucleotides selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7,8, 9, and 10, or a complement thereof, which oligonucleotide has 100 orfewer nucleotides. In another embodiment, the present disclosureprovides an oligonucleotide that includes a nucleic acid having at least70% sequence identity (e.g., at least 75%, 80%, 85%, 90% or 95%, etc.)to one of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, or acomplement thereof, which oligonucleotide has 100 or fewer nucleotides.Generally, these oligonucleotides may be primer nucleic acids, probenucleic acids, or the like in these embodiments. In certain of theseembodiments, the oligonucleotides have 40 or fewer nucleotides (e.g. 35or fewer nucleotides, 30 or fewer nucleotides, etc.) In someembodiments, the oligonucleotides comprise at least one modifiednucleotide, e.g. to alter nucleic acid hybridization stability relativeto unmodified nucleotides. Optionally, the oligonucleotides comprise atleast one label and/or at least one quencher moiety. In someembodiments, the oligonucleotides include at least one conservativelymodified variation. “Conservatively modified variations” or, simply,“conservative variations” of a particular nucleic acid sequence refersto those nucleic acids, which encode identical or essentially identicalamino acid sequences, or, where the nucleic acid does not encode anamino acid sequence, to essentially identical sequences. One of skillwill recognize that individual substitutions, deletions or additionswhich alter, add or delete a single amino acid or a small percentage ofamino acids (typically less than 5%, more typically less than 4%, 2% or1%) in an encoded sequence are “conservatively modified variations”where the alterations result in the deletion of an amino acid, additionof an amino acid, or substitution of an amino acid with a chemicallysimilar amino acid.

In one aspect, amplification can employ a polymerase enzyme having 5′ to3′ nuclease activity. Thus, the first and second fluorescent moietiesmay be within no more than 8 nucleotides of each other along the lengthof the probe. In another aspect, the mecC-MRSA probes includes a nucleicacid sequence that permits secondary structure formation. Such secondarystructure formation generally results in spatial proximity between thefirst and second fluorescent moiety. According to this method, thesecond fluorescent moiety on the probe can be a quencher.

The present disclosure provides for methods of detecting the presence orabsence of mecC-MRSA in a biological sample from an individual. Suchmethods generally include performing at least one cycling step, whichincludes an amplifying step and a dye-binding step. Typically, theamplifying step includes contacting the sample with a plurality of pairsof mecC-MRSA primers to produce one or more mecC-MRSA amplificationproducts if a mecC-MRSA nucleic acid molecule is present in the sample,and the dye-binding step includes contacting the mecC-MRSA amplificationproduct with a double-stranded DNA binding dye. Such methods alsoinclude detecting the presence or absence of binding of thedouble-stranded DNA binding dye into the amplification product, whereinthe presence of binding is indicative of the presence of mecC-MRSA inthe sample, and wherein the absence of binding is indicative of theabsence of mecC-MRSA in the sample. A representative double-stranded DNAbinding dye is ethidium bromide. In addition, such methods also caninclude determining the melting temperature between the mecC-MRSAamplification product and the double-stranded DNA binding dye, whereinthe melting temperature confirms the presence or absence of mecC-MRSA.

In a further embodiment, a kit for detecting one or more nucleic acidsof mecC-MRSA is provided. The kit can include a plurality of sets ofmecC-MRSA primers specific for amplification of the mecC gene target;and one or more detectable mecC-MRSA probes specific for detection ofthe mecC-MRSA amplification products.

In one aspect, the kit can include probes already labeled with donor andcorresponding acceptor fluorescent moieties, or can include fluorophoricmoieties for labeling the probes. The kit can also include nucleosidetriphosphates, nucleic acid polymerase, and buffers necessary for thefunction of the nucleic acid polymerase. The kit can also include apackage insert and instructions for using the primers, probes, andfluorophoric moieties to detect the presence or absence of mecC-MRSA ina sample.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present subject matter, suitable methods andmaterials are described below. In addition, the materials, methods, andexamples are illustrative only and not intended to be limiting. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedrawings and detailed description, and from the claims.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows PCR growth curves of experiments using several primersspecific for mecC MRSA compared with a primer (RE2) specific for mecAcontaining MRSA.

FIG. 2 shows PCR growth curves of experiments using three differentprimers specific for mecC MRSA. Two primers (AHREMECC01 and AHREMECC03)show similar growth curve performance with respect to fluorescence andelbow value. The third primer (AHREMECC02) had reduced fluorescence anddelayed elbow values.

FIG. 3 shows PCR growth curves of experiments using several primersspecific for mecC MRSA, all with similar growth curve performance.

FIG. 4 shows a schematic diagram of MRSA typing based on RE (rightextremity of SCCmec) typing.

DETAILED DESCRIPTION OF THE INVENTION

Diagnosis of mecC-MRSA infection by nucleic acid amplification providesa method for rapidly and accurately detecting the bacterial infection. Areal-time assay for detecting mecC-MRSA in a sample is described herein.Primers and probes for detecting mecC-MRSA are provided, as are articlesof manufacture or kits containing such primers and probes. The increasedsensitivity of real-time PCR for detection of mecC-MRSA compared toother methods, as well as the improved features of real-time PCRincluding sample containment and real-time detection of the amplifiedproduct, make feasible the implementation of this technology for routinediagnosis of mecC-MRSA infections in the clinical laboratory.

Similar to mecA, the homolog methicillin-resistance gene, mecC, encodesan altered methicillin-resistant penicillin-binding protein (PBP2a orPBP2′), a penicillin binding protein with reduced affinity for β-lactamrings (the primary active-site of the β-lactam antibiotics such aspenicillins, cephalosporins and carbapenems) (Guignard et al., 2005,Curr Opin Pharmacol 5 (5): 479-89), that is not present in susceptiblestrains and is believed to have been acquired from a distantly relatedspecies. MecC is carried on a mobile genetic element, the StaphylococcalChromosomal Cassette mec (SCCmec) of MRSA strains. SCC elements alsooccur in sensitive S. aureus but do not carry the mecC gene or carry anon-functional mecC gene. Such strains can be a source of false positiveresults, because they may have the same right extremity junction.

However, MRSA detection from nasal specimen by detecting the mecC geneand a S. aureus specific gene leads to low positive predictive values(PPV) due to the presence of varying amounts of both non-resistant S.aureus and methicillin-resistant coagulase-negative Staphylococci(MRCoNS). A combination of those is undistinguishable from MRSA, becauseof the presence of both targets. Depending on the prevalence of MRSAthis situation leads up to 30% false positive results. For a better PPV,the chosen target needs to be unique for MRSA. The only target currentlyknown is Staphylococcal Chromosomal Cassette (SCCmec), which amplifiesthe transposon integration site for the genetic element carrying themecC gene.

SCCmec, the SCC element of MRSA (with functional mecC gene), is atransposon of highly variable length (16 kb-67 kb) integrated into the3′ portion of the open reading frame X from S. aureus (orfX) containingthe mecC gene. OrfX has no defined function in S. aureus and is uniqueto S. aureus. The integration of SCCmec creates a signature unique toMRSA.

SCCmec elements have two essential components; the ccr gene complex(ccr) and the mec gene complex (mec). The ccr gene complex is composedof ccr genes and surrounding open reading frames (ORFs), and the mecgene complex is composed of the mecC gene, regulatory genes, andinsertion sequences upstream or downstream of mecC.

Classification of MRSA can be based on different genotypes of MRSA. Onetarget for MRSA detection and classification based on genotypes may bethe right extremity junction (RE) of the SCCmec. This method of MRSAtyping relates is therefore called RE (right extremity of SCCmec)typing. This typing method takes advantage of the polymorphism at theright extremity of SCCmec DNAs adjacent to the integration site amongthe different types of SCCmec.

The detection of mecC-containing S. aureus (mecC-MRSA) utilizes astrategy to produce an amplicon at the RE junction between the S. aureusorfX gene and SCCmec carrying the mecC gene which confers resistance tomethicillin. To accomplish this, one primer is anchored in a highlyconserved region of the orfX gene of S. aureus (orfX primer), and asecond primer is located within the non-conserved RE junction of SCCmec(RE primer or mecC-MRSA primer). The resulting amplicon from the twoprimers spans part of the orfX gene and part of SCCmec. Due to thenon-homologous nature of SCCmec at the RE junction, several different REprimers are necessary in order to accomplish the most coverage of uniqueMRSA strains carrying mecC genes. In the present disclosure, thespecific sequence of the RE region of MRSA carrying mecC was determinedfor 14 unique mecC strains, and RE primers were designed from thosesequences for inclusive detection of the mecC carrying MRSA strains. Todetect the resulting amplicons, one or more detectable mecC-MRSA probesmay be utilized wherein the mecC-MRSA probes include a sequence that canpartially or entirely hybridize to a portion of the amplicon at alocation containing the highly conserved region of the orfX gene. Theprimers can be used in a kit for detection of mecC-MRSA, which can alsoinclude a multiplex for inclusive detection of MRSA carrying mecA ormecC genes.

The disclosed methods may include performing at least one cycling stepthat includes amplifying one or more portions of mecC-MRSA nucleic acidmolecule gene target from a sample using one or more pairs of mecC-MRSAprimers. “mecC-MRSA primers” as used herein refer to oligonucleotideprimers that specifically anneal to nucleic acid sequence encoding mecCin MRSA in the non-conserved RE junction of SCCmec, and initiate DNAsynthesis therefrom under appropriate conditions. Each of the discussedmecC-MRSA primers anneals to a target within or adjacent to therespective mecC-MRSA target nucleic acid molecule such that at least aportion of each amplification product contains nucleic acid sequencecorresponding to the target. The one or more of mecC amplificationproducts are produced provided that one or more of mecC nucleic acid ispresent in the sample, thus the presence of the one or more of mecCamplification products is indicative of the presence of mecC-MRSA in thesample. The amplification product should contain the nucleic acidsequences that are complementary to one or more detectable probes formecC-MRSA. Each cycling step includes an amplification step, ahybridization step, and a detection step, in which the sample iscontacted with the one or more detectable probes for mecC-MRSA fordetection of the presence or absence of mecC-MRSA in the sample.

As used herein, the term “amplifying” refers to the process ofsynthesizing nucleic acid molecules that are complementary to one orboth strands of a template nucleic acid molecule (e.g., mecC).Amplifying a nucleic acid molecule typically includes denaturing thetemplate nucleic acid, annealing primers to the template nucleic acid ata temperature that is below the melting temperatures of the primers, andenzymatically elongating from the primers to generate an amplificationproduct. Amplification typically requires the presence ofdeoxyribonucleoside triphosphates, a DNA polymerase enzyme (e.g.,Platinum® Taq) and an appropriate buffer and/or co-factors for optimalactivity of the polymerase enzyme (e.g., MgCl₂ and/or KCl).

The term “primer” is used herein as known to those skilled in the artand refers to oligomeric compounds, primarily to oligonucleotides butalso to modified oligonucleotides that are able to “prime” DNA synthesisby a template-dependent DNA polymerase, i.e., the 3′-end of the, e.g.,oligonucleotide provides a free 3′-OH group whereto further“nucleotides” may be attached by a template-dependent DNA polymeraseestablishing 3′ to 5′ phosphodiester linkage whereby deoxynucleosidetriphosphates are used and whereby pyrophosphate is released. Therefore,there is—except possibly for the intended function—no fundamentaldifference between a “primer”, an “oligonucleotide”, or a “probe”.

The term “hybridizing” refers to the annealing of one or more probes toan amplification product. Hybridization conditions typically include atemperature that is below the melting temperature of the probes but thatavoids non-specific hybridization of the probes.

The term “5′ to 3′ nuclease activity” refers to an activity of a nucleicacid polymerase, typically associated with the nucleic acid strandsynthesis, whereby nucleotides are removed from the 5′ end of nucleicacid strand.

The term “thermostable polymerase” refers to a polymerase enzyme that isheat stable, i.e., the enzyme catalyzes the formation of primerextension products complementary to a template and does not irreversiblydenature when subjected to the elevated temperatures for the timenecessary to effect denaturation of double-stranded template nucleicacids. Generally, the synthesis is initiated at the 3′ end of eachprimer and proceeds in the 5′ to 3′ direction along the template strand.Thermostable polymerases have been isolated from Thermus flavus, T.ruber, T. thermophilus, T. aquaticus, T. lacteus, T. rubens, Bacillusstearothermophilus, and Methanothermus fervidus. Nonetheless,polymerases that are not thermostable also can be employed in PCR assaysprovided the enzyme is replenished.

The term “complement thereof” refers to nucleic acid that is both thesame length as, and exactly complementary to, a given nucleic acid.

The term “extension” or “elongation” when used with respect to nucleicacids refers to when additional nucleotides (or other analogousmolecules) are incorporated into the nucleic acids. For example, anucleic acid is optionally extended by a nucleotide incorporatingbiocatalyst, such as a polymerase that typically adds nucleotides at the3′ terminal end of a nucleic acid.

The terms “identical” or percent “identity” in the context of two ormore nucleic acid sequences, refer to two or more sequences orsubsequences that are the same or have a specified percentage ofnucleotides that are the same, when compared and aligned for maximumcorrespondence, e.g., as measured using one of the sequence comparisonalgorithms available to persons of skill or by visual inspection.Exemplary algorithms that are suitable for determining percent sequenceidentity and sequence similarity are the BLAST programs, which aredescribed in, e.g., Altschul et al. (1990) “Basic local alignment searchtool” J. Mol. Biol. 215:403-410, Gish et al. (1993) “Identification ofprotein coding regions by database similarity search” Nature Genet.3:266-272, Madden et al. (1996) “Applications of network BLAST server”Meth. Enzymol. 266:131-141, Altschul et al. (1997) “Gapped BLAST andPSI-BLAST: a new generation of protein database search programs” NucleicAcids Res. 25:3389-3402, and Zhang et al. (1997) “PowerBLAST: A newnetwork BLAST application for interactive or automated sequence analysisand annotation” Genome Res. 7:649-656, which are each incorporatedherein by reference.

A “modified nucleotide” in the context of an oligonucleotide refers toan alteration in which at least one nucleotide of the oligonucleotidesequence is replaced by a different nucleotide that provides a desiredproperty to the oligonucleotide. Exemplary modified nucleotides that canbe substituted in the oligonucleotides described herein include, e.g., aC5-methyl-dC, a C5-ethyl-dC, a C5-methyl-dU, a C5-ethyl-dU, a2,6-diaminopurine, a C5-propynyl-dC, a C5-propynyl-dU, a C7-propynyl-dA,a C7-propynyl-dG, a C5-propargylamino-dC, a C5-propargylamino-dU, aC7-propargylamino-dA, a C7-propargylamino-dG, a7-deaza-2-deoxyxanthosine, a pyrazolopyrimidine analog, a pseudo-dU, anitro pyrrole, a nitro indole, 2′-0-methyl Ribo-U, 2′-0-methyl Ribo-C,an N4-ethyl-dC, an N6-methyl-dA, and the like. Many other modifiednucleotides that can be substituted in the oligonucleotides are referredto herein or are otherwise known in the art. In certain embodiments,modified nucleotide substitutions modify melting temperatures (Tm) ofthe oligonucleotides relative to the melting temperatures ofcorresponding unmodified oligonucleotides. To further illustrate,certain modified nucleotide substitutions can reduce non-specificnucleic acid amplification (e.g., minimize primer dimer formation or thelike), increase the yield of an intended target amplicon, and/or thelike in some embodiments. Examples of these types of nucleic acidmodifications are described in, e.g., U.S. Pat. No. 6,001,611, which isincorporated herein by reference.

MecC-Containing Staphylococcus aureus (mecC-MRSA)

The present disclosure provides methods to detect mecC-MRSA byamplifying, for example, a portion of the mecC nucleic acid sequence.Nucleic acid sequences of SCCmec of various subtypes of mecC-MRSA areavailable (e.g., GenBank Accession No. FR823292). Specifically, primersand probes to amplify and detect mecC-MRSA nucleic acid molecule targetsare provided by the embodiments in the present disclosure.

For detection of mecC-MRSA, primers and probes to amplify the mecC-MRSARE junctions are provided. MecC-MRSA nucleic acids other than thoseexemplified herein can also be used to detect mecC-MRSA in a sample. Forexample, functional variants can be evaluated for specificity and/orsensitivity by those of skill in the art using routine methods.Representative functional variants can include, e.g., one or moredeletions, insertions, and/or substitutions in the mecC-MRSA nucleicacids disclosed herein.

More specifically, embodiments of the oligonucleotides each include anucleic acid with a sequence selected from SEQ ID NOs: 1, 2, 3, 4, 5, 6,7, 8, 9, and 10, a substantially identical variant thereof in which thevariant has at least, e.g., 80%, 90%, or 95% sequence identity to one ofSEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10, or a complement of SEQ IDNOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 and the variant.

TABLE I  MecC-MRSA Primers and Probe SEQ SEQUENCE ID NO  1 mecC-MRSA5′-TCTTACTATCAAAAAGATTGATAACTCT Primer CGC-3′  2 mecC-MRSA5′-CTCTTTTAGTTTCTATGTACTTTCTTAC Primer TATCAA-3′  3 mecC-MRSA5′-GAATATCAAGTAACATCTCAGCAATGAT Primer AC-3′  4 mecC-MRSA5′-ATCTGTATAAAATAGATTAGTCCTTTAT Primer TGCGTA-3′  5 mecC-MRSA5′-TAGTAAGTGAGGTTGCTGAAATTGTACT Primer A-3′  6 mecC-MRSA5′-CAATTCTCATAAACCTCATACGTAAAG Primer A-3′  7 mecC-MRSA5′-ACGGCAATTCTCATAAACCTCA-3′ Primer  8 mecC-MRSA5′-ACTCTCGCAAAACATAACGGC-3′ Primer  9 orfX Primer5′-GAAATACAAGGAAAGATGCTATCTTC C-3′ 10 (orfX) mecC 5′-TTGAACCAACGCATGACCCAAGGGC-3′ MRSA Probe

TABLE II AMPLICONS SEQ ID NO SEQUENCE 115′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGA-3′ 125′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTA AGAAAGTACATAGAAACTAAAAGAG-3′13 5′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCGCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATCAGAGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGAAAGTACATAGAAACTAAAAGAGTATTTTTATCTACAATAGCATTTATAATTTATTCTATTATTGTATACTTTATTTTAATTATTAGTATCATTGCTGAGATGTTACTTGATATTC-3′ 145′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGAAATGTACATAGAAACTAAAAGAGTATTTTTATCTACAATAGCATTTATAATTTATTCTATTATTGTATACTTTATTTTAATTATTAGTATCATGCTGAGATGTTACTTGATATTCTATGTCTATTTTTTAGGAAATTCTATACTATTAAAATTATGGTATTTTATACGCAATAA AGGACTAATCTATTTTATACAGAT-3′15 5′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGCAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGAAAGTACATAGAAACTAAAAGAGTATTTTTATCTACAATAGCATTTATAATTTATTCTATTATTGTATACTTTATTTTAATTATTAGTATCATTGCTGAGATGTTACTTGATATTCTATGTCTATTTTTTAGGAAATTCTATACTATTAAAATTATGGTATTTTATACGCAATAAAGGACTAATCTATTTTATACAGATTAGTCCTTTATTGTAGTCTTTAAAAACTAGTTACTCATTAATATTTTTTAGTACAATTTCAG CAACCTCACTTACTA-3′ 165′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTAACAACGCAGTAACTACGCACTATCATTCAGCAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTG-3′ 175′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCC GT-3′ 185′-GAAATACAAGGAAAGATGCTATCTTCCGAAGGATTGGCCCAAGAATTGAACCAACGCATGACCCAAGGGCAAAGCGACTTTGTATTCGTCATTGGCGGATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCC GTTATGTTTTGCGAGAGT-3′

In one embodiment, the above described sets of mecC-MRSA primers andprobes are used in order to provide for detection of mecC-MRSA in abiological sample suspected of containing mecC-MRSA. The sets of primersand probes may comprise or consist the primers and probes specific forthe mecC-MRSA RE junction nucleic acid sequences, comprising orconsisting of the nucleic acid sequences of SEQ ID NOs: 1, 2, 3, 4, 5,6, 7, 8, 9, and 10. In another embodiment, the primers and probes forthe mecC-MRSA targets comprise or consist of a functionally activevariant of any of the primers and probes of SEQ ID NOs: 1, 2, 3, 4, 5,6, 7, 8, 9, and 10.

A functionally active variant of any of the primers and/or probes of SEQID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 may be identified by using theprimers and/or probes in the disclosed methods. A functionally activevariant of a primer and/or probe of any of the SEQ ID NOs: 1, 2, 3, 4,5, 6, 7, 8, 9, and 10 pertains to a primer and/or probe which provides asimilar or higher specificity and sensitivity in the described method orkit as compared to the respective sequence of SEQ ID NOs: 1, 2, 3, 4, 5,6, 7, 8, 9, and 10.

The variant may, e.g., vary from the sequence of SEQ ID NOs: 1, 2, 3, 4,5, 6, 7, 8, 9, and 10 by one or more nucleotide additions, deletions orsubstitutions such as one or more nucleotide additions, deletions orsubstitutions at the 5′ end and/or the 3′ end of the respective sequenceof SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10. As detailed above, aprimer (and/or probe) may be chemically modified, i.e., a primer and/orprobe may comprise a modified nucleotide or a non-nucleotide compound. Aprobe (or a primer) is then a modified oligonucleotide. “Modifiednucleotides” (or “nucleotide analogs”) differ from a natural“nucleotide” by some modification but still consist of a base orbase-like compound, a pentofuranosyl sugar or a pentofuranosylsugar-like compound, a phosphate portion or phosphate-like portion, orcombinations thereof. For example, a “label” may be attached to the baseportion of a “nucleotide” whereby a “modified nucleotide” is obtained. Anatural base in a “nucleotide” may also be replaced by, e.g., a7-desazapurine whereby a “modified nucleotide” is obtained as well. Theterms “modified nucleotide” or “nucleotide analog” are usedinterchangeably in the present application. A “modified nucleoside” (or“nucleoside analog”) differs from a natural nucleoside by somemodification in the manner as outlined above for a “modified nucleotide”(or a “nucleotide analog”).

Oligonucleotides including modified oligonucleotides and oligonucleotideanalogs that amplify a nucleic acid molecule encoding the mecC-MRSA REjunction nucleic acid sequences, e.g., nucleic acids encodingalternative portions of mecC-MRSA RE junctions can be designed using,for example, a computer program such as OLIGO (Molecular BiologyInsights Inc., Cascade, Colo.). Important features when designingoligonucleotides to be used as amplification primers include, but arenot limited to, an appropriate size amplification product to facilitatedetection (e.g., by electrophoresis), similar melting temperatures forthe members of a pair of primers, and the length of each primer (i.e.,the primers need to be long enough to anneal with sequence-specificityand to initiate synthesis but not so long that fidelity is reducedduring oligonucleotide synthesis). Typically, oligonucleotide primersare 8 to 50 nucleotides in length (e.g., 8, 10, 12, 14, 16, 18, 20, 22,24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, or 50 nucleotides inlength).

In addition to a set of primers, the methods may use one or more probesin order to detect the presence or absence of mecC-MRSA. The term“probe” refers to synthetically or biologically produced nucleic acids(DNA or RNA), which by design or selection, contain specific nucleotidesequences that allow them to hybridize under defined predeterminedstringencies specifically (i.e., preferentially) to “target nucleicacids”, in the present case to a mecC-MRSA (target) nucleic acid. A“probe” can be referred to as a “detection probe” meaning that itdetects the target nucleic acid.

In some embodiments, the described mecC-MRSA probes can be labeled withat least one fluorescent label. In one embodiment, the mecC-MRSA probescan be labeled with a donor fluorescent moiety, e.g., a fluorescent dye,and a corresponding acceptor fluorescent moiety, e.g., a quencher.

In one embodiment, the probe comprises or consists of a fluorescentmoiety and the nucleic acid sequences comprise or consist of SEQ ID NO:10 (shown without the label).

Designing oligonucleotides to be used as probes can be performed in amanner similar to the design of primers. Embodiments may use a singleprobe or a pair of probes for detection of the amplification product.Depending on the embodiment, the probe(s) use may comprise at least onelabel and/or at least one quencher moiety. As with the primers, theprobes usually have similar melting temperatures, and the length of eachprobe must be sufficient for sequence-specific hybridization to occurbut not so long that fidelity is reduced during synthesis.Oligonucleotide probes are generally 15 to 30 (e.g., 16, 18, 20, 21, 22,23, 24, or 25) nucleotides in length.

Constructs can include vectors each containing one of mecC-MRSA REjunction primers and probes nucleic acid molecules (e.g., SEQ ID NOs: 1,2, 3, 4, 5, 6, 7, 8, 9, and 10). Constructs can be used, for example, ascontrol template nucleic acid molecules. Vectors suitable for use arecommercially available and/or produced by recombinant nucleic acidtechnology methods routine in the art. MecC-MRSA nucleic acid moleculescan be obtained, for example, by chemical synthesis, direct cloning frommecC-MRSA, or by PCR amplification.

Constructs suitable for use in the methods typically include, inaddition to the mecC-MRSA nucleic acid molecules (e.g., a nucleic acidmolecule that contains one or more sequences of SEQ ID NOs: 1, 2, 3, 4,5, 6, 7, 8, 9, and 10), sequences encoding a selectable marker (e.g., anantibiotic resistance gene) for selecting desired constructs and/ortransformants, and an origin of replication. The choice of vectorsystems usually depends upon several factors, including, but not limitedto, the choice of host cells, replication efficiency, selectability,inducibility, and the ease of recovery.

Constructs containing mecC-MRSA nucleic acid molecules can be propagatedin a host cell. As used herein, the term host cell is meant to includeprokaryotes and eukaryotes such as yeast, plant and animal cells.Prokaryotic hosts may include E. coli, Salmonella typhimurium, Serratiamarcescens, and Bacillus subtilis. Eukaryotic hosts include yeasts suchas S. cerevisiae, S. pombe, Pichia pastoris, mammalian cells such as COScells or Chinese hamster ovary (CHO) cells, insect cells, and plantcells such as Arabidopsis thaliana and Nicotiana tabacum. A constructcan be introduced into a host cell using any of the techniques commonlyknown to those of ordinary skill in the art. For example, calciumphosphate precipitation, electroporation, heat shock, lipofection,microinjection, and viral-mediated nucleic acid transfer are commonmethods for introducing nucleic acids into host cells. In addition,naked DNA can be delivered directly to cells (see, e.g., U.S. Pat. Nos.5,580,859 and 5,589,466).

Polymerase Chain Reaction (PCR)

U.S. Pat. Nos. 4,683,202, 4,683,195, 4,800,159, and 4,965,188 discloseconventional PCR techniques. PCR typically employs two oligonucleotideprimers that bind to a selected nucleic acid template (e.g., DNA orRNA). Primers useful in some embodiments include oligonucleotidescapable of acting as points of initiation of nucleic acid synthesiswithin the described mecC-MRSA nucleic acid sequences (e.g., SEQ ID NOs:1, 2, 4, 5, 7, 8, and 9). A primer can be purified from a restrictiondigest by conventional methods, or it can be produced synthetically. Theprimer is preferably single-stranded for maximum efficiency inamplification, but the primer can be double-stranded. Double-strandedprimers are first denatured, i.e., treated to separate the strands. Onemethod of denaturing double stranded nucleic acids is by heating.

If the template nucleic acid is double-stranded, it is necessary toseparate the two strands before it can be used as a template in PCR.Strand separation can be accomplished by any suitable denaturing methodincluding physical, chemical or enzymatic means. One method ofseparating the nucleic acid strands involves heating the nucleic aciduntil it is predominately denatured (e.g., greater than 50%, 60%, 70%,80%, 90% or 95% denatured). The heating conditions necessary fordenaturing template nucleic acid will depend, e.g., on the buffer saltconcentration and the length and nucleotide composition of the nucleicacids being denatured, but typically range from about 90° C. to about105° C. for a time depending on features of the reaction such astemperature and the nucleic acid length. Denaturation is typicallyperformed for about 30 sec to 4 min (e.g., 1 min to 2 min 30 sec, or 1.5min).

If the double-stranded template nucleic acid is denatured by heat, thereaction mixture is allowed to cool to a temperature that promotesannealing of each primer to its target sequence on the describedmecC-MRSA nucleic acid molecules. The temperature for annealing isusually from about 35° C. to about 65° C. (e.g., about 40° C. to about60° C.; about 45° C. to about 50° C.). Annealing times can be from about10 sec to about 1 min (e.g., about 20 sec to about 50 sec; about 30 secto about 40 sec). The reaction mixture is then adjusted to a temperatureat which the activity of the polymerase is promoted or optimized, i.e.,a temperature sufficient for extension to occur from the annealed primerto generate products complementary to the template nucleic acid. Thetemperature should be sufficient to synthesize an extension product fromeach primer that is annealed to a nucleic acid template, but should notbe so high as to denature an extension product from its complementarytemplate (e.g., the temperature for extension generally ranges fromabout 40° C. to about 80° C. (e.g., about 50° C. to about 70° C.; about60° C.). Extension times can be from about 10 sec to about 5 min (e.g.,about 30 sec to about 4 min; about 1 min to about 3 min; about 1 min 30sec to about 2 min).

PCR assays can employ mecC-MRSA nucleic acid such as RNA or DNA (cDNA).The template nucleic acid need not be purified; it may be a minorfraction of a complex mixture, such as mecC-MRSA nucleic acid containedin human cells. MecC-MRSA nucleic acid molecules may be extracted from abiological sample by routine techniques such as those described inDiagnostic Molecular Microbiology: Principles and Applications (Persinget al. (eds), 1993, American Society for Microbiology, Washington D.C.).Nucleic acids can be obtained from any number of sources, such asplasmids, or natural sources including bacteria, yeast, viruses,organelles, or higher organisms such as plants or animals.

The oligonucleotide primers (e.g., SEQ ID NOs: 1, 2, 4, 5, 7, 8, and 9)are combined with PCR reagents under reaction conditions that induceprimer extension. For example, chain extension reactions generallyinclude 50 mM KCl, 10 mM Tris-HCl (pH 8.3), 15 mM MgCl₂, 0.001% (w/v)gelatin, 0.5-1.0 μg denatured template DNA, 50 pmoles of eacholigonucleotide primer, 2.5 U of Taq polymerase, and 10% DMSO). Thereactions usually contain 150 to 320 μM each of dATP, dCTP, dTTP, dGTP,or one or more analogs thereof.

The newly synthesized strands form a double-stranded molecule that canbe used in the succeeding steps of the reaction. The steps of strandseparation, annealing, and elongation can be repeated as often as neededto produce the desired quantity of amplification products correspondingto the target mecC-MRSA nucleic acid molecules. The limiting factors inthe reaction are the amounts of primers, thermostable enzyme, andnucleoside triphosphates present in the reaction. The cycling steps(i.e., denaturation, annealing, and extension) are preferably repeatedat least once. For use in detection, the number of cycling steps willdepend, e.g., on the nature of the sample. If the sample is a complexmixture of nucleic acids, more cycling steps will be required to amplifythe target sequence sufficient for detection. Generally, the cyclingsteps are repeated at least about 20 times, but may be repeated as manyas 40, 60, or even 100 times.

Fluorescence Resonance Energy Transfer (FRET)

FRET technology (see, for example, U.S. Pat. Nos. 4,996,143, 5,565,322,5,849,489, and 6,162,603) is based on a concept that when a donorfluorescent moiety and a corresponding acceptor fluorescent moiety arepositioned within a certain distance of each other, energy transfertakes place between the two fluorescent moieties that can be visualizedor otherwise detected and/or quantitated. The donor typically transfersthe energy to the acceptor when the donor is excited by light radiationwith a suitable wavelength. The acceptor typically re-emits thetransferred energy in the form of light radiation with a differentwavelength. In certain systems, non-fluorescent energy can betransferred between donor and acceptor moieties, by way of biomoleculesthat include substantially non-fluorescent donor moieties (see, forexample, U.S. Pat. No. 7,741,467).

In one example, a oligonucleotide probe can contain a donor fluorescentmoiety and a corresponding quencher, which may or not be fluorescent,and which dissipates the transferred energy in a form other than light.When the probe is intact, energy transfer typically occurs between thetwo fluorescent moieties such that fluorescent emission from the donorfluorescent moiety is quenched. During an extension step of a polymerasechain reaction, a probe bound to an amplification product is cleaved bythe 5′ to 3′ nuclease activity of, e.g., a Taq Polymerase such that thefluorescent emission of the donor fluorescent moiety is no longerquenched. Exemplary probes for this purpose are described in, e.g., U.S.Pat. Nos. 5,210,015, 5,994,056, and 6,171,785. Commonly useddonor-acceptor pairs include the FAM-TAMRA pair. Commonly used quenchersare DABCYL and TAMRA. Commonly used dark quenchers include BlackHoleQuenchers™ (BHQ), (Biosearch Technologies, Inc., Novato, Calif.), IowaBlack™, (Integrated DNA Tech., Inc., Coralville, Iowa), BlackBerry™Quencher 650 (BBQ-650), (Berry & Assoc., Dexter, Mich.).

In another example, two oligonucleotide probes, each containing afluorescent moiety, can hybridize to an amplification product atparticular positions determined by the complementarity of theoligonucleotide probes to the mecC-MRSA target nucleic acid sequence.Upon hybridization of the oligonucleotide probes to the amplificationproduct nucleic acid at the appropriate positions, a FRET signal isgenerated. Hybridization temperatures can range from about 35° C. toabout 65° C. for about 10 sec to about 1 min.

Fluorescent analysis can be carried out using, for example, a photoncounting epifluorescent microscope system (containing the appropriatedichroic mirror and filters for monitoring fluorescent emission at theparticular range), a photon counting photomultiplier system, or afluorimeter. Excitation to initiate energy transfer, or to allow directdetection of a fluorophore, can be carried out with an argon ion laser,a high intensity mercury (Hg) arc lamp, a fiber optic light source, orother high intensity light source appropriately filtered for excitationin the desired range.

As used herein with respect to donor and corresponding acceptorfluorescent moieties “corresponding” refers to an acceptor fluorescentmoiety having an absorbance spectrum that overlaps the emission spectrumof the donor fluorescent moiety. The wavelength maximum of the emissionspectrum of the acceptor fluorescent moiety should be at least 100 nmgreater than the wavelength maximum of the excitation spectrum of thedonor fluorescent moiety. Accordingly, efficient non-radiative energytransfer can be produced therebetween.

Fluorescent donor and corresponding acceptor moieties are generallychosen for (a) high efficiency Forster energy transfer; (b) a largefinal Stokes shift (>100 nm); (c) shift of the emission as far aspossible into the red portion of the visible spectrum (>600 nm); and (d)shift of the emission to a higher wavelength than the Raman waterfluorescent emission produced by excitation at the donor excitationwavelength. For example, a donor fluorescent moiety can be chosen thathas its excitation maximum near a laser line (for example,Helium-Cadmium 442 nm or Argon 488 nm), a high extinction coefficient, ahigh quantum yield, and a good overlap of its fluorescent emission withthe excitation spectrum of the corresponding acceptor fluorescentmoiety. A corresponding acceptor fluorescent moiety can be chosen thathas a high extinction coefficient, a high quantum yield, a good overlapof its excitation with the emission of the donor fluorescent moiety, andemission in the red part of the visible spectrum (>600 nm).

Representative donor fluorescent moieties that can be used with variousacceptor fluorescent moieties in FRET technology include fluorescein,Lucifer Yellow, B-phycoerythrin, 9-acridineisothiocyanate, LuciferYellow VS, 4-acetamido-4′-isothiocyanatostilbene-2,2′-disulfonic acid,7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin, succinimdyl1-pyrenebutyrate, and4-acetamido-4′-isothiocyanatostilbene-2,2′-disulfonic acid derivatives.Representative acceptor fluorescent moieties, depending upon the donorfluorescent moiety used, include LC Red 640, LC Red 705, Cy5, Cy5.5,Lissamine rhodamine B sulfonyl chloride, tetramethyl rhodamineisothiocyanate, rhodamine x isothiocyanate, erythrosine isothiocyanate,fluorescein, diethylenetriamine pentaacetate, or other chelates ofLanthanide ions (e.g., Europium, or Terbium). Donor and acceptorfluorescent moieties can be obtained, for example, from Molecular Probes(Junction City, Oreg.) or Sigma Chemical Co. (St. Louis, Mo.).

The donor and acceptor fluorescent moieties can be attached to theappropriate probe oligonucleotide via a linker arm. The length of eachlinker arm is important, as the linker arms will affect the distancebetween the donor and acceptor fluorescent moieties. The length of alinker arm can be the distance in Angstroms (Å) from the nucleotide baseto the fluorescent moiety. In general, a linker arm is from about 10 Åto about 25 Å. The linker arm may be of the kind described in WO84/03285. WO 84/03285 also discloses methods for attaching linker armsto a particular nucleotide base, and also for attaching fluorescentmoieties to a linker arm.

An acceptor fluorescent moiety, such as an LC Red 640, can be combinedwith an oligonucleotide which contains an amino linker (e.g., C6-aminophosphoramidites available from ABI (Foster City, Calif.) or GlenResearch (Sterling, Va.)) to produce, for example, LC Red 640-labeledoligonucleotide. Frequently used linkers to couple a donor fluorescentmoiety such as fluorescein to an oligonucleotide include thiourealinkers (FITC-derived, for example, fluorescein-CPG's from Glen Researchor ChemGene (Ashland, Mass.)), amide-linkers(fluorescein-NHS-ester-derived, such as CX-fluorescein-CPG from BioGenex(San Ramon, Calif.)), or 3′-amino-CPGs that require coupling of afluorescein-NHS-ester after oligonucleotide synthesis.

Detection of mecC-MRSA

The present disclosure provides methods for detecting the presence orabsence of mecC-MRSA in a biological or non-biological sample. Methodsprovided avoid problems of sample contamination, false negatives, andfalse positives. The methods include performing at least one cyclingstep that includes amplifying a portion of mecC-MRSA target nucleic acidmolecules from a sample using a plurality of pairs of mecC-MRSA primers,and a FRET detecting step. Multiple cycling steps are performed,preferably in a thermocycler. Methods can be performed using themecC-MRSA primers and probes to detect the presence of mecC-MRSA, andthe detection of mecC-MRSA indicates the presence of mecC-MRSA in thesample.

As described herein, amplification products can be detected usinglabeled hybridization probes that take advantage of FRET technology. OneFRET format utilizes TaqMan® technology to detect the presence orabsence of an amplification product, and hence, the presence or absenceof mecC-MRSA. TaqMan® technology utilizes one single-strandedhybridization probe labeled with, e.g., one fluorescent dye and onequencher, which may or may not be fluorescent. When a first fluorescentmoiety is excited with light of a suitable wavelength, the absorbedenergy is transferred to a second fluorescent moiety according to theprinciples of FRET. The second fluorescent moiety is generally aquencher molecule. During the annealing step of the PCR reaction, thelabeled hybridization probe binds to the target DNA (i.e., theamplification product) and is degraded by the 5′ to 3′ nuclease activityof, e.g., the Taq Polymerase during the subsequent elongation phase. Asa result, the fluorescent moiety and the quencher moiety becomespatially separated from one another. As a consequence, upon excitationof the first fluorescent moiety in the absence of the quencher, thefluorescence emission from the first fluorescent moiety can be detected.By way of example, an ABI PRISM® 7700 Sequence Detection System (AppliedBiosystems) uses TaqMan® technology, and is suitable for performing themethods described herein for detecting the presence or absence ofmecC-MRSA in the sample.

Molecular beacons in conjunction with FRET can also be used to detectthe presence of an amplification product using the real-time PCRmethods. Molecular beacon technology uses a hybridization probe labeledwith a first fluorescent moiety and a second fluorescent moiety. Thesecond fluorescent moiety is generally a quencher, and the fluorescentlabels are typically located at each end of the probe. Molecular beacontechnology uses a probe oligonucleotide having sequences that permitsecondary structure formation (e.g., a hairpin). As a result ofsecondary structure formation within the probe, both fluorescentmoieties are in spatial proximity when the probe is in solution. Afterhybridization to the target nucleic acids (i.e., amplificationproducts), the secondary structure of the probe is disrupted and thefluorescent moieties become separated from one another such that afterexcitation with light of a suitable wavelength, the emission of thefirst fluorescent moiety can be detected.

Another common format of FRET technology utilizes two hybridizationprobes. Each probe can be labeled with a different fluorescent moietyand are generally designed to hybridize in close proximity to each otherin a target DNA molecule (e.g., an amplification product). A donorfluorescent moiety, for example, fluorescein, is excited at 470 nm bythe light source of the LightCycler® Instrument. During FRET, thefluorescein transfers its energy to an acceptor fluorescent moiety suchas LightCycler®-Red 640 (LC Red 640) or LightCycler®-Red 705 (LC Red705). The acceptor fluorescent moiety then emits light of a longerwavelength, which is detected by the optical detection system of theLightCycler® instrument. Efficient FRET can only take place when thefluorescent moieties are in direct local proximity and when the emissionspectrum of the donor fluorescent moiety overlaps with the absorptionspectrum of the acceptor fluorescent moiety. The intensity of theemitted signal can be correlated with the number of original target DNAmolecules (e.g., the number of mecC-MRSA genomes). If amplification ofmecC-MRSA target nucleic acid occurs and an amplification product isproduced, the step of hybridizing results in a detectable signal basedupon FRET between the members of the pair of probes.

Generally, the presence of FRET indicates the presence of mecC-MRSA inthe sample, and the absence of FRET indicates the absence of mecC-MRSAin the sample. Inadequate specimen collection, transportation delays,inappropriate transportation conditions, or use of certain collectionswabs (calcium alginate or aluminum shaft) are all conditions that canaffect the success and/or accuracy of a test result, however. Using themethods disclosed herein, detection of FRET within, e.g., 45 cyclingsteps is indicative of an mecC-MRSA infection.

Representative biological samples that can be used in practicing themethods include, but are not limited to dermal swabs, nasal swabs, woundswabs, blood cultures, skin, and soft tissue infections. Collection andstorage methods of biological samples are known to those of skill in theart. Biological samples can be processed (e.g., by nucleic acidextraction methods and/or kits known in the art) to release mecC-MRSAnucleic acid or in some cases, the biological sample can be contacteddirectly with the PCR reaction components and the appropriateoligonucleotides.

Melting curve analysis is an additional step that can be included in acycling profile. Melting curve analysis is based on the fact that DNAmelts at a characteristic temperature called the melting temperature(Tm), which is defined as the temperature at which half of the DNAduplexes have separated into single strands. The melting temperature ofa DNA depends primarily upon its nucleotide composition. Thus, DNAmolecules rich in G and C nucleotides have a higher Tm than those havingan abundance of A and T nucleotides. By detecting the temperature atwhich signal is lost, the melting temperature of probes can bedetermined. Similarly, by detecting the temperature at which signal isgenerated, the annealing temperature of probes can be determined. Themelting temperature(s) of the mecC-MRSA probes from the mecC-MRSAamplification products can confirm the presence or absence of mecC-MRSAin the sample.

Within each thermocycler run, control samples can be cycled as well.Positive control samples can amplify target nucleic acid controltemplate (other than described amplification products of target genes)using, for example, control primers and control probes. Positive controlsamples can also amplify, for example, a plasmid construct containingthe target nucleic acid molecules. Such a plasmid control can beamplified internally (e.g., within the sample) or in a separate samplerun side-by-side with the patients' samples using the same primers andprobe as used for detection of the intended target. Such controls areindicators of the success or failure of the amplification,hybridization, and/or FRET reaction. Each thermocycler run can alsoinclude a negative control that, for example, lacks target template DNA.Negative control can measure contamination. This ensures that the systemand reagents would not give rise to a false positive signal. Therefore,control reactions can readily determine, for example, the ability ofprimers to anneal with sequence-specificity and to initiate elongation,as well as the ability of probes to hybridize with sequence-specificityand for FRET to occur.

In an embodiment, the methods include steps to avoid contamination. Forexample, an enzymatic method utilizing uracil-DNA glycosylase isdescribed in U.S. Pat. Nos. 5,035,996, 5,683,896 and 5,945,313 to reduceor eliminate contamination between one thermocycler run and the next.

Conventional PCR methods in conjunction with FRET technology can be usedto practice the methods. In one embodiment, a LightCycler® instrument isused. The following patent applications describe real-time PCR as usedin the LightCycler® technology: WO 97/46707, WO 97/46714, and WO97/46712.

The LightCycler® can be operated using a PC workstation and can utilizea Windows NT operating system. Signals from the samples are obtained asthe machine positions the capillaries sequentially over the opticalunit. The software can display the fluorescence signals in real-timeimmediately after each measurement. Fluorescent acquisition time is10-100 milliseconds (msec). After each cycling step, a quantitativedisplay of fluorescence vs. cycle number can be continually updated forall samples. The data generated can be stored for further analysis.

As an alternative to FRET, an amplification product can be detectedusing a double-stranded DNA binding dye such as a fluorescent DNAbinding dye (e.g., SYBR® Green or SYBR® Gold (Molecular Probes)). Uponinteraction with the double-stranded nucleic acid, such fluorescent DNAbinding dyes emit a fluorescence signal after excitation with light at asuitable wavelength. A double-stranded DNA binding dye such as a nucleicacid intercalating dye also can be used. When double-stranded DNAbinding dyes are used, a melting curve analysis is usually performed forconfirmation of the presence of the amplification product.

It is understood that the embodiments of the present disclosure are notlimited by the configuration of one or more commercially availableinstruments.

Articles of Manufacture/Kits

Embodiments of the present disclosure further provide for articles ofmanufacture or kits to detect mecC-MRSA. An article of manufacture caninclude primers and probes used to detect mecC-MRSA, together withsuitable packaging materials. Representative primers and probes fordetection of mecC-MRSA are capable of hybridizing to mecC-MRSA targetnucleic acid molecules. In addition, the kits may also include suitablypackaged reagents and materials needed for DNA immobilization,hybridization, and detection, such solid supports, buffers, enzymes, andDNA standards. Methods of designing primers and probes are disclosedherein, and representative examples of primers and probes that amplifyand hybridize to mecC-MRSA target nucleic acid molecules are provided.

Articles of manufacture can also include one or more fluorescentmoieties for labeling the probes or, alternatively, the probes suppliedwith the kit can be labeled. For example, an article of manufacture mayinclude a donor and/or an acceptor fluorescent moiety for labeling themecC-MRSA probes. Examples of suitable FRET donor fluorescent moietiesand corresponding acceptor fluorescent moieties are provided above.

Articles of manufacture can also contain a package insert or packagelabel having instructions thereon for using the mecC-MRSA primers andprobes to detect mecC-MRSA in a sample. Articles of manufacture mayadditionally include reagents for carrying out the methods disclosedherein (e.g., buffers, polymerase enzymes, co-factors, or agents toprevent contamination). Such reagents may be specific for one of thecommercially available instruments described herein.

Embodiments of the present disclosure will be further described in thefollowing examples, which do not limit the scope of the inventiondescribed in the claims.

EXAMPLES

The following examples and figures are provided to aid the understandingof the subject matter, the true scope of which is set forth in theappended claims. It is understood that modifications can be made in theprocedures set forth without departing from the spirit of the invention.

Example I MecC-MRSA Gene Targets

Referring to FIGS. 1 to 3, the oligo sets #1-8 were evaluated withreference sequence LGA251 Accession No. FR823292.

MecC-MRSA Oligo Set #1 Up Primer: (SEQ ID NO: 9)GAAATACAAGGAAAGATGCTATCTTCJ (J = t-butylbenzyl dC) Dn Primer:(SEQ ID NO: 1) TCTTACTATCAAAAAGATTGATAACTCTCGJ (J = t-butylbenzyl dC)Probe: (SEQ ID NO: 10)

(E = thHEX, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #1: (SEQ ID NO: 11)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGA MecC-MRSA Oligo Set #2:Up Primer: (SEQ ID NO: 9) GAAATACAAGGAAAGATGCTATCTTCJ (J =t-butylbenzyl dC) Dn Primer: (SEQ ID NO: 2)CTCTTTTAGTTTCTATGTACTTTCTTACTATCAJ (J = t-butylbenzyl dA) Probe:(SEQ ID NO: 10)

(E = thHEX, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #2: (SEQ ID NO: 12)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGAAAGT ACATAGAAACTAAAAGAGMecC-MRSA Oligo Set #3: (SEQ ID NO: 9) Up Primer:GAAATACAAGGAAAGATGCTATCTTCJ (J = t-butylbenzyl dA) Dn Primer:(SEQ ID NO: 3) GAATATCAAGTAACATCTCAGCAATGATAJ (J = t-butylbenzyl dC)Probe: (SEQ ID NO: 10)

(E = thHEX, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #3: (SEQ ID NO: 13)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGAAAGTACATAGAAACTAAAAGAGTATTTTTATCTACAATAGCATTTATAATTTATTCTATTATTGTATACTTTATTTTAATTATTAGTATCATTGCTGAGATG TTACTTGATATTCMecC-MRSA Oligo Set #4: Up Primer: (SEQ ID NO: 9)GAAATACAAGGAAAGATGCTATCTTCJ (J = t-butylbenzyl dC) Dn Primer:(SEQ ID NO: 4) ATCTGTATAAAATAGATTAGTCCTTTATTGCGTJ (J = t-butylbenzyl dA)Probe: (SEQ ID NO: 10)

(E = thHEX, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #4: (SEQ ID NO: 14)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGAAAGTACATAGAAACTAAAAGAGTATTTTTATCTACAATAGCATTTATAATTTATTCTATTATTGTATACTTTATTTTAATTATTAGTATCATTGCTGAGATGTTACTTGATATTCTATGTCTATTTTTTAGGAAATTCTATACTATTAAAATTATGGTATTTTATACGCAATAAAGGACTAATCTATTTTATACAGAT MecC-MRSA Oligo Set #5:Up Primer: (SEQ ID NO: 9) GAAATACAAGGAAAGATGCTATCTTCJ (J =t-butylbenzyl dC) Dn Primer: (SEQ ID NO: 5)TAGTAAGTGAGGTTGCTGAAATTGTACTJ (J = t-butylbenzyl dA) Probe:(SEQ ID NO: 10)

(E = thHEX (E = thFAM, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #5: (SEQ ID NO: 15)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAATTGCCGTTATGTTTTGCGAGAGTTATCAATCTTTTTGATAGTAAGAAAGTACATAGAAACTAAAAGAGTATTTTTATCTACAATAGCATTTATAATTTATTCTATTATTGTATACTTTATTTTAATTATTAGTATCATTGCTGAGATGTTACTTGATATTCTATGTCTATTTTTTAGGAAATTCTATACTATTAAAATTATGGTATTTTATACGCAATAAAGGACTAATCTATTTTATACAGATTAGTCCTTTATTGTAGTCTTTAAAAACTAGTTACTCATTAATATTTTTTAGTACAATTTCAGCAACCTCACTTACTA MecC-MRSA Oligo Set #6: Up Primer:(SEQ ID NO: 9) GAAATACAAGGAAAGATGCTATCTTCT (J = t-butylbenzyl dC)Dn Primer: (SEQ ID NO: 6) CAATTCTCATAAACTTCATACGTAAAGJ (J =t-butylbenzyl dA) Probe: (SEQ ID NO: 10)

(E = thHEX, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #6: (SEQ ID NO: 16)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAAT TGMecC-MRSA Oligo Set #7: Up Primer: (SEQ ID NO: 9)GAAATACAAGGAAAGATGCTATCTTCT (J = t-butylbenzyl dC) Dn Primer:(SEQ ID NO: 7) ACGGCAATTCTCATAAACCTCJ (J = t-butylbenzyl dA) Probe:(SEQ ID NO: 10)

(E = thHEX, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #7: (SEQ ID NO: 17)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAAT TGCCGTMecC-MRSA Oligo Set #8: Up Primer: (SEQ ID NO: 9)GAAATACAAGGAAAGATGCTATCTTCJ (J = t-butylbenzyl dC) Dn Primer:(SEQ ID NO: 8) ACTCTCGCAAAACATAACGGJ (J = t-butylbenzyl dC) Probe:(SEQ ID NO: 10)

(E = thHEX, Q = BHQ2, P = 3′ phosphate)Amplicon generated from Oligo Set #8: (SEQ ID NO: 18)

ATCAAATGGCCTGCACAAGGACGTCTTACAACGCAGTAACTACGCACTATCATTCAGCAAAATGACATTTCCACATCAAATGATGCGGGTTGTGTTAATTGAGCAAGTGTATAGAGCGTTTAAGATTATGCGCGGAGAAGCGTATCACAAATGATGCGGTTTTTTTAACCTCTTTACGTATGAGGTTTATGAGAAT TGCCGTTATGTTTTGCGAGAGT

While the foregoing invention has been described in some detail forpurposes of clarity and understanding, it will be clear to one skilledin the art from a reading of this disclosure that various changes inform and detail can be made without departing from the true scope of theinvention. For example, all the techniques and apparatus described abovecan be used in various combinations. All publications, patents, patentapplications, and/or other documents cited in this application areincorporated by reference in their entirety for all purposes to the sameextent as if each individual publication, patent, patent application,and/or other document were individually indicated to be incorporated byreference for all purposes.

What is claimed:
 1. A method of detecting mecC-containing Staphylococcusaureus (mecC-MRSA) in a sample, the method comprising: performing anamplifying step comprising contacting the sample with an orfX primer anda mecC-MRSA primer to produce an amplification product if mecC-MRSA ispresent in the sample; performing a hybridizing step comprisingcontacting the amplification product with one or more detectablemecC-MRSA probes; and detecting the presence or absence of the amplifiedproduct, wherein the presence of the amplified product is indicative ofthe presence of mecC-MRSA in the sample and wherein the absence of theamplified product is indicative of the absence of mecC-MRSA in thesample; wherein the mecC-MRSA primer comprises a sequence selected fromthe group consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, and 8, or acomplement thereof.
 2. The method of claim 1, wherein: the hybridizingstep comprises contacting the amplification product with a probe that islabeled with a donor fluorescent moiety and a corresponding acceptorfluorescent moiety; and the detecting step comprises detecting thepresence or absence of fluorescence resonance energy transfer (FRET)between the donor fluorescent moiety and the acceptor fluorescent moietyof the probe, wherein the presence or absence of fluorescence isindicative of the presence or absence of mecC-MRSA in the sample.
 3. Themethod of claim 1, wherein the detectable mecC-MRSA probe comprises thesequence of SEQ ID NO: 10, or a complement thereof.
 4. The method ofclaim 2, wherein said amplification employs a polymerase enzyme having5′ to 3′ nuclease activity.
 5. The method of claim 2, wherein the donorfluorescent moiety and the corresponding acceptor fluorescent moiety arewithin no more than 8 nucleotides of each other on the probe.
 6. Themethod of claim 2, wherein the acceptor fluorescent moiety is aquencher.
 7. A kit for detecting a nucleic acid of mecC-containingStaphylococcus aureus (mecC-MRSA) comprising: a first oligonucleotidecomprising a sequence selected from the group consisting of SEQ ID NOs:1, 2, 3, 4, 5, 6, 7, and 8, or a complement thereof, or a complementthereof; a second oligonucleotide configured to hybridize to a portionof an orfX gene; and a third detectably labeled oligonucleotideconfigured to hybridize to an amplicon generated by the firstoligonucleotide and the second oligonucleotide.
 8. The kit of claim 7,wherein the third detectably labeled oligonucleotide comprises a donorfluorescent moiety and a corresponding acceptor fluorescent moiety. 9.The kit of claim 8, wherein the acceptor fluorescent moiety is aquencher.
 10. The kit of claim 7, further comprising nucleosidetriphosphates, nucleic acid polymerase, and buffers necessary for thefunction of the nucleic acid polymerase.
 11. An oligonucleotidecomprising a sequence of oligonucleotides selected from the groupconsisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, and 8, or a complementthereof.
 12. The oligonucleotide of claim 11, wherein theoligonucleotide comprises at least one modified nucleotide.
 13. Theoligonucleotide of claim 11, wherein the oligonucleotide has 40 or fewernucleotides.